You know, that's what I like about this forum, You can't get away with anything, of course you are both right the hull portholes don't look right, because they are the wrong way round the large flange looks ridiculous, so have decided to do something about it, It would have bugged the hell out of me anyway.
Using a counterbore bit I tried boring out one of the alloy portlights on the old wheelhouse, and found the heat from boring released the glue and it popped out, so I did the ones in the hull and got them all out without any damage at all.
I've ordered some 3/16" brass portholes which equates to a 9" glass area in real terms, which I'm going to settle for, and the holes in the new wheelhouse I'll fill and re bore to fit the smaller ports.
Thanks to you both for giving your honest opinion, ultimately I'll be happier with the build.